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Complete Genome Analysis of Gluconacetobacter Xylinus CGMCC

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Complete Genome Analysis of Gluconacetobacter Xylinus CGMCC www.nature.com/scientificreports OPEN Complete genome analysis of Gluconacetobacter xylinus CGMCC 2955 for elucidating bacterial Received: 8 November 2017 Accepted: 3 April 2018 cellulose biosynthesis and Published: xx xx xxxx metabolic regulation Miao Liu1, Lingpu Liu1, Shiru Jia1, Siqi Li1, Yang Zou2 & Cheng Zhong1 Complete genome sequence of Gluconacetobacter xylinus CGMCC 2955 for fne control of bacterial cellulose (BC) synthesis is presented here. The genome, at 3,563,314 bp, was found to contain 3,193 predicted genes without gaps. There are four BC synthase operons (bcs), among which only bcsI is structurally complete, comprising bcsA, bcsB, bcsC, and bcsD. Genes encoding key enzymes in glycolytic, pentose phosphate, and BC biosynthetic pathways and in the tricarboxylic acid cycle were identifed. G. xylinus CGMCC 2955 has a complete glycolytic pathway because sequence data analysis revealed that this strain possesses a phosphofructokinase (pf)-encoding gene, which is absent in most BC-producing strains. Furthermore, combined with our previous results, the data on metabolism of various carbon sources (monosaccharide, ethanol, and acetate) and their regulatory mechanism of action on BC production were explained. Regulation of BC synthase (Bcs) is another efective method for precise control of BC biosynthesis, and cyclic diguanylate (c-di-GMP) is the key activator of BcsA–BcsB subunit of Bcs. The quorum sensing (QS) system was found to positively regulate phosphodiesterase, which decomposed c-di-GMP. Thus, in this study, we demonstrated the presence of QS in G. xylinus CGMCC 2955 and proposed a possible regulatory mechanism of QS action on BC production. Bacterial cellulose (BC), naturally produced by several species of Acetobacter, is a strong and ultra-pure form of cellulose1. It has the same chemical structure as plant cellulose but is devoid of hemicellulose and lignin2. Until now, many researchers have endeavoured to control BC production to realise its potential applications. Most applications have been implemented by optimizing the carbon source and culture conditions3,4. Additionally, functionalisation or modifcation of BC has mainly been achieved via chemical or mechanical modifcations of the cellulose matrix5,6. Nowadays, synthetic biology enables model microorganisms to be easily reprogrammed with modular DNA code to perform a variety of new tasks for useful purposes7. Tis approach may allow for more fnely tuned control over BC synthesis by gene regulation. Nonetheless, only a few attempts at genetic engineering have been made for BC-producing bacteria, and the toolkit for genetic modifcation has hardly been described8. Tus, it is essential for researchers to gain genomic insights into various BC-producing strains. So far, several BC-producing Gluconacetobacter (Komagataeibacter) species have been sequenced, and the genomes of K. xylinus E259, K. medellinensis NBRC 3288 (ref.10), K. nataicola RZS0111, and Gluconobacter oxy- dans DSM 3504 were sequenced completely. Gluconacetobacter xylinus (formerly Acetobacter xylinum) is one of the most commonly studied species because of its ability to produce relatively large amounts of BC from a wide range of carbon and nitrogen sources in liquid culture3,4,12 and has become the most popular strain so far for manufacturing of various materials, including paper13, food packaging14, medical materials15, and cell culture16. It is difcult to obtain high productivity by means of G. xylinus in a large-scale fermentation system owing to its low yield under agitated culture. Nonetheless, BC secreted by G. xylinus has unique properties including high 1Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China. 2Tianjin Jialihe Livestock Group Co., Ltd, JinWei Road, Beichen District, Tianjin, 300402, P. R. China. Correspondence and requests for materials should be addressed to C.Z. (email: chzhong. [email protected]) SCIENTIFIC REPORTS | (2018) 8:6266 | DOI:10.1038/s41598-018-24559-w 1 www.nature.com/scientificreports/ Genome size (bp) 3,563,314 Gap N (bp) 0 GC content (%) 63.29 Total genes 3,139 Non-coding RNA 117 rRNA 45 tRNA 57 others 15 Repeat DNAs SINEs 13 LINEs 9 LTR 0 DNA elements 6 Small RNA 41 Satellites 0 Simple repeats 409 Low complexity 38 Table 1. General features of G. xylinus CGMCC 2955 genome. SINEs: short interspersed elements. LINEs: long interspersed nuclear elements. LTR: long terminal repeat. quality in terms of mechanical strength, water-holding capacity, crystallinity, biodegradability, and biocompat- ibility17. G. xylinus CGMCC 2955 originates from the fermentation substrates of vinegar18. It has been studied as a model organism for BC production for decades and has been successfully applied to production of wound dressings19,20. In the current study, we present a complete genome sequence of G. xylinus CGMCC 2955 to provide background information for genetic engineering so that precise control of BC biosynthesis can be achieved on the basis of the metabolic pathway that we proposed previously3. A comparison of the arrangement and composition of BC synthase operons (bcs) with those of other BC-producing strains was performed. Furthermore, the relation between the bcs operon and quorum sensing (QS) system – a widely studied system for population regulation – is discussed. Results Sequencing showed that the genome is 3,563,314 bp long with GC content of 63.29%. One scafold was obtained without gaps (Table 1). Gene prediction and annotation of the G. xylinus CGMCC 2955 genome resulted in 3,193 predicted genes. Amongst 117 non-coding RNAs, there are 45 rRNAs, 57 tRNAs, and 15 other RNAs. In the repeat DNAs, simple repeats turned out to be the most abundant repeat families, accounting for 0.51% of the G. xylinus CGMCC 2955 genome, followed by small RNA, accounting for 0.20% of the genome. Non–long terminal repeats were also identifed in the genome and contain 13 short interspersed nuclear elements and nine long interspersed nuclear elements. Besides, six DNA transposons (fve DNA/hAT-Ac specimens and one DNA/ TcMar-Tigger) were detected. No long terminal repeats or satellites were observed. Te cluster of orthologous groups (COG) function-based classifcation of G. xylinus CGMCC 2955 genes revealed 23 functional groups, in which 19.96% of the genes are functionally uncharacterised (Fig. 1). Te second and third largest functional groups were ‘transcription’ and ‘amino acid transport and metabolism’; they consisted of 988 and 985 genes, respectively. Carbon source metabolism. A total of 50 genes of transporters, 13 genes of symporters, and 50 genes of permeases were identifed in the genome of G. xylinus CGMCC 2955. Tey are responsible for the transport of sugars (e.g. glucose, arabinose, and galactose), sugar acids (e.g. gluconate, α-ketoglutarate, and galactonate), amino acids, spermidines, vitamin B12, phosphate, metal ions, and lipopolysaccharide. G. xylinus CGMCC 2955 is capable of producing BC from several carbon sources3. Generally, glucose (Glc) is metabolised through the Embden–Meyerhof–Parnas (EMP) pathway, which has proven to be incomplete in most BC-producing stains because of the lack of a gene encoding phosphofructokinase (PFK; EC 2.7.1.11)11,21,22. Of note, according to the gene sequence analysis, the G. xylinus CGMCC 2955 genome possesses a gene encoding phosphofructokinase B (pfB, CT154_09360), while there is no gene encoding phosphofructokinase A (pfA). Te other two key enzymes are glucokinase (GK) and pyruvate kinase (PK), whose encoding gene locus tags are CT154_11525 and CT154_15810, respectively. Te pentose phosphate pathway (PPP) is another efective glucose metabolic pathway in G. xylinus. In the G. xylinus CGMCC 2955 genome, genes encoding glucose-6-phosphate dehydrogenase (6pgd, CT154_14710), glucose-6-phosphate 1-dehydrogenase (6pgd-1, CT154_14205 and CT154_05345), 6-phosphogluconolactonase (6pgl, CT154_14190), 6-phosphogluconate dehydrogenase (6pgad, CT154_14210), ribose-5-phosphate isomerase A (rpi A, CT154_14185), ribulose-phosphate 3-epimerase (rpe, CT154_13290), transketolase (tkt, CT154_07695, CT154_08455, CT154_12910, and CT154_14220), and transal- dolase (tsd, CT154_07690 and CT154_14215) were identifed. Gluconic acid (GlcA) is an important by-product of BC production in G. xylinus3,23. It was found to be produced from glucose by glucose dehydrogenase (gd, CT154_01250 and CT154_06665) and can be converted to 6-phosphogluconate (GlcA6P) by gluconokinase (GntK). Tere are two genes encoding GntK (CT154_14180 and CT154_03305), and the latter was hypothesised SCIENTIFIC REPORTS | (2018) 8:6266 | DOI:10.1038/s41598-018-24559-w 2 www.nature.com/scientificreports/ Figure 1. Cluster of orthologous groups (COG) classifcation of protein functions. Figure 2. BC production from ethanol and acetate as the sole or supplementary carbon sources. (None: no carbon source, Act: acetate, Eth: ethanol, Glu: glucose). to encode a thermosensitive GntK. Te tricarboxylic acid cycle (TCA) has three key enzymes – citrate synthase (CT154_06205), isocitrate dehydrogenase (CT154_11710 and CT154_00570), and 2-oxoglutarate dehydrogenase (CT154_14680) – and the genes coding for these enzymes are all present in G. xylinus CGMCC 2955. Fructose (FRU) and glycerol (GLY) can considerably contribute to a BC yield just as glucose can3. Via catalysis by fruc- tokinase (frk, CT154_06355), fructose was found to be converted to fructose-6-phosphate (F6P). When glyc- erol was utilised
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